All That's Left Behind
by moviegal101
Summary: Neal has never been one to reveal his past - especially if someone in his past doesn't want him to do so. When he joins the Bureau he learns that no matter how hard you try to protect someone, sometimes their secrets just won't stay hidden and the past can come back with a vengeance.
1. Prologue

_Inside the relatively nice Manhattan loft, a young woman took off her coat with a sigh. It had been a long day at work and all she wanted to do was collapse in her bed and not wake up again for at least 2 months. Her eyes shifted to the pile of papers, both on her coffee table and in the black messenger bag hanging on her chair. She sighed and pushed back her hair tiredly. After a moment, she took out her phone from her coat pocket and turned the screen on. No missed messages. _

_She unloaded her bag and placed the files waiting for her on the table with the others, laying her phone within easy reach next to them. Not wanting to focus on the work in front of her, she pushed it aside and got to her feet. Wandering to the kitchen, she opened her fridge and pulled out some leftover Chinese food. As she stuck it in the microwave she heard her phone buzzing in the other room. With a groan she headed to answer it, sure that it was her boss with even more work for her to finish before the next morning. Without even looking at the screen she hit the "talk" button._

"_Yes?" she said._

_There was silence before the voice on the other end said quietly, "It's me."_

_The woman immediately recognized the voice and looked at the screen. "Number Blocked." Of course. _

"_What's going on? Are you alright?" she asked worriedly. _

"_Why wouldn't I be?" said the voice, slightly defensive. _

_The young woman laughed and said teasingly, "You never call me. Why now?"_

"_Just wanted to check up on you," came the short response. _

_The woman looked disappointed, pursing her lips as she saw through the lie. "Right… So, how have you been?"_

"_Alright I suppose. Bit quiet without you guys around."_

"_I'm sorry. I've just been so busy with work. But how's…?"_

"_He's fine," came the answer, a bit too quickly. "I saw him yesterday."_

_The young woman smiled. "I'm glad. I'm sure he really appreciates your visits. I'm sorry I haven't been able to come with you." There was silence and then the young woman asked in a low voice, "Does he still think I turned him in?"_

_There was a sigh on the end of the line. "I'm not sure what he thinks, to be honest. We don't talk about you much."_

_The young woman fought back the sudden rush of tears. "I didn't know it was him, you have to believe me," she pleaded. She shook her head as if the woman on the other end of the phone could see her. _

_There was silence once more. "I know," came the answer finally. "I believe you." Then in a voice so quiet it was almost to herself: "I have to." _

"_Sorry?" asked the young woman, confused. _

"_Nothing. I just mean… I have to believe that there is still some good in the world, you know? Even in our lives. Our type of lives."_

_The young woman's voice tightened. "I was never part of your life. And even if I was, I gave that up a long time ago. You know that."_

_There was a pause. "I know. But it will always be there with you. Trust me. You can't run. No matter what happens, loyalty always wins."_

"_Are you alright?" asked the young woman, alarmed at how hollow the other voice sounded. _

_A thread of desperation and urgency snaked its way in. "It's… I'm fine. But I need to ask you something."_

"_Of course." It came out as more of a statement rather than an offer. The young woman waited, her breath suspended as she listened._

_There was long pause on the other line and then out of nowhere came, "Do you know where he hid the treasure?"_

_The young woman was stunned. "What? I- No, I- He never told me, I never asked." Her brow furrowed. "Why do you need to know?"_

"_That's not important" came the quick answer. "He told me it was in San Diego, that's all. But what if it was a test? I need to know for sure."_

"_Why would he do that to you?" demanded the young woman. "He loved you, he wouldn't lie to you. If he told you it was in San Diego…" She faltered. "But why do you need to know? Are you in trouble again?" Without waiting for an answer, she continued. "I can help you. Just tell me if you're in some kind of trouble, if you need money! Do you owe money to someone? Is someone coming after you? I have connections, we can fix this. Just let me help you!" _

"_I don't need your help," came the voice from the other line. Earlier it was hollow, evasive, but now it was cold and distant. "I have to go. But before I do, could you do me a favor?"_

"_Of course," said the young woman, wanting to help in any way. "What do you need?"_

"_Look out for him. He's being released in eight weeks. Keep an eye on him? Make sure he doesn't do anything stupid, fall back into old ruts." There was a pause. "Please."_

_The young woman sat frozen. "What? Wh- Why? Why can't you?" she asked in a daze, not liking where this was going._

"_I think yesterday was my last visit for a while," said the woman on the other line. The young woman in the apartment opened her mouth but before she could the other woman cut her off. "Don't try and stop me. I know you, I know what you're going to say."_

"_Wait!" the young woman pleaded into her phone. "Don't go. I know what you're planning on doing. Don't run. Let me help you!"_

"_Goodbye," came the answer. Then a click. Then nothing. _

_The young woman slowly took the phone from her ear, stunned. Leaving her food in the microwave she flipped through a couple of files on her table to take her mind off things but soon snapped then shut again. Something was wrong but she couldn't put her finger on it. Rubbing her eyes an enormous yawn reminded her how tired she was. Letting her eyelids close she made a note to herself to look up her friend tomorrow and see where she had been and try to put the pieces of the puzzle together and figure out what exactly was going on._

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**Hope you enjoy! Please let me know what you think, if you have suggestions, etc. I would love to hear from you!**

**~moviegal101~**


	2. Chapter 1

**250 views of the first chapter. Wow. **

**Chloe: Thank you so much for your review! I'm glad you're liking the story and I hope you keep reading!  
**

** ocgirlfr (Sorry, it wouldn't let me add the period in your name) : I appreciated your review. I hope you like where I take the story and you'll find out more about that phone call. Bear in mind, as I'm sure you know, with Neal nothing is ever as it seems! **

**Note: these first few chapters do have dialogue from the show. I do not own the rights to the show! There will be much more original writing once the characters, situations, and relationships are established. Bear with me for a few chapters. **

**I hope you enjoy!  
**

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"Drop 3."

A middle-aged man, clearly in charge, let out a nervous breath. One false move and the whole thing would explode, putting him, his men, and the mission in danger.

"Drop 2," came the voice just outside the vault the FBI was trying to open.

It was only a three-digit code and all was going well so far.

"Drop 4," came the last number. "All pins down, preparing to open."

Looking relieved, the man let out a breath. But something still felt wrong. A young woman across the room started forward, a worried look on her face. Her eyes flickered to the man in charge.

"What's wrong?" he asked with trepidation.

The woman paused, narrowing his eyes. It was too easy. Something was off. Picking up on her worry, the man started to think. "3-2-4" he muttered to himself, the young woman doing the same.

"3-2-4!" said the man, suddenly sounding panicked. He began to move towards the vault. "Wait!"

The young woman looked at him and started to follow. She still didn't know what the significance was, but they needed to warn the safe cracker to get out before something drastic happened. With no warning, the vault suddenly exploded, the blast stopping just before the group of FBI agents in the next room.

"Everybody keep back" yelled the man, holding out an arm to prevent anybody from rushing in towards the vault.

"Are you okay?" he shouted, rushing into the next room, looking for the safe cracker.

"Peter!" choked the young woman, hurrying after him.

"Stay there, Emma!" he shouted back, rendering her to a halt.

Peter breathed a sigh of thankfulness as he found the safe cracker unharmed. He ushered him out, still holding a handkerchief to his nose. For a moment, all the agents in the room were reduced to doubling over, coughing in the dust. Then Peter straightened up angrily.

"What happened?" asked the safe cracker, bewildered.

"I said '_wait,_' you didn't wait!" replied Peter, the anger in his voice brought on more from a fear of what could have befallen them and thankfully didn't. "10,000 man hours to get this close to the Dutchman and you blow up evidence!"

One of the agents stepped forward. "Agent Burke, how'd you know it was going to do that?" he wanted to know.

It was Clifton Jones, one of Peter's favorite agents. He hadn't been around for long, but it was clear he was a competent, loyal, and promising agent and Peter found his optimism and humor refreshing.

"3-2-4," came the reply. "Look at your phones," he said to the agents at large.

They looked at him blankly. "What's it spell?" he prompted them.

"Oh," said Jones, having figured it out.

"F-B-I," said Emma grimly.

"Yeah," deadpanned Peter. "_F-B-I_."

"Apparently he knew we were coming," replied Jones, not really seeming all that concerned, a fact Peter picked up on.

"Ya think so, Copernicus?" he shot at the agent.

"_Peter_!" admonished Emma firmly. "It was a valid statement, try to calm down. We made a mistake but we'll get him eventually. You know we will."

A somewhat guilty looking Peter glanced at Jones with an apologetic look. Jones held up his hands in an accepting manner. Peter continued brushing himself off, picking something off of his shoulder.

"Somebody wanna tell me what this is?" he asked, holding up a fiber of some kind, tinted red but reflecting black. "Huh? Anybody?"

The agents all looked at him blankly again. Emma suspected that Jones knew but he seemed reluctant to open his mouth again.

"Nobody knows what it is?" pressed Peter.

Emma glanced at Jones and he looked back at her and nodded slightly, confirming her theory.

"Great, look at you," Peter went off on a tangent. Jones started to speak in order to answer and hopefully save them from a lecture but ultimately thought better of it and closed his mouth.

"How many of you went to Harvard?" continued Peter.

About half raised their hands. Peter looked like he regretted the question the moment it was out of his mouth and said quickly, "_Don't_ raise your hands… Don't-"

His attention was pulled to a young woman walking in with shoulder length black hair and a pretty face, looking around her as though she wasn't sure of what had happened. The young woman made eye contact with Emma and nodded a greeting, which Emma returned with a smile.

"Ah, Diana," said Peter, sounding relieved. "Look at this. Apparently our boy has a sense of humor," he said dryly.

Emma rolled her eyes. Diana didn't respond but just looked at Peter and took a deep breath. She seemed reluctant to say anything and Emma edged closer to hear.

"Neal Caffrey escaped," she finally said.

Peter stared at her. Emma stood frozen, wide-eyed. The rest of the agents shifted and suddenly seemed uneasy, catching Diana's words despite her attempt to conceal them. Neal had been on the run for several years before Peter had tracked him down and arrested him, a fact Emma was all too aware of. Most of her knowledge even the FBI didn't know she knew, having obtained it in rather unconventional ways. Not that she'd tell Peter that. Or anyone, unless it was absolutely necessary. Too many question about how she knew Neal and too much of that would ultimately lead into what she knew about his girlfriend, Kate. Those were stories and questions for another time, preferably never.

Peter stared at Diana for a moment. "Come with me," he said grimly.

He and Diana started to walk out of the room, leaving the agents muttering among themselves.

"I'll be right back," murmured Emma to Jones.

She followed Peter and Diana into the hallway leading out of the bank, staying far enough away to avoid attracting attention to herself but close enough to hear what was being said and to deter bank employees stopping her from following.

"What's this?" asked Peter, looking at a file Diana had given him.

"US Marshals are requesting your help," she replied, dusting his suit off.

"My help?" asked Peter, surprised.

"Director Thompson asked for you personally," informed Diana.

Despite the fascinating conversation between Peter and Diana, Emma's attention was caught by the file. She needed to see what was inside.

"Of course he would, Peter" added Emma, quickening her stride. "You did catch him last time. The Marshals were on a duck hunt if I remember correctly. You're the best agent we have." She added a smile, hoping to soften him up but knowing full well that he would see through it.

And sure enough: "Here," he said bluntly, handing her the file. "This is what you want, right? Take it."

Emma complied while Diana smiled. She liked Emma well enough, and vice versa. Both were intelligent, capable women, something each respected about the other. That's not to say that there weren't arguments, but for the most part things went smoothly. There just wasn't room or time for things as petty as that in the Bureau.

"What do you know about Caffrey?" Peter asked Emma, in his _give me the details_ voice.

"Not much," Emma replied, flipping though the file. Names jumped out at her, most of which were familiar. _Kate Moreau. Alexandra Hunter. Sara Ellis. Nick Halden. Vincent Adler. Matthew Keller. _ "Do we know why he ran?"

"I'll let the Marshals explain," replied Diana. "They didn't give me much to tell you. They want you there right away," she added to Peter.

Emma looked up at Peter, an eyebrow raised in question. He looked at her and sighed.

"You can come if you can get past customs, since Diana can't accompany me," he said grudgingly. "I just don't want you getting into trouble."

"Please. Do I ever?"

Peter shot her a look and Emma looked away, suddenly very fascinated with the file once more. Diana smothered a laugh and without warning, Peter started walking.

"I'd watch out if I were. Peter could easily ship you off to a Washington desk job," said Diana with a smile.

Emma laughed. "I'll be fine," she said. "Peter would miss me too much if I weren't around."

Diana laughed too and then became sober. "Emma, I should probably tell you something," she began, but was interrupted by Peter calling in an annoyed voice, "Emma! Are you coming or not?!"

"On my way!" she called back. "Can we talk later?" she asked, apologetically to Diana.

"Of course," the agent replied.

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**Let me know what you think!**

**I have posted a picture of what Emma looks like in my head on my home page. Check it out if you want. If you have a picture of her in your mind that you like better, definitely go with that!**

**Thank you for reading! **

**~moviegal101~**


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